Happy New Years
Jan. 1st, 2004 10:21 am![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
catsittingstillWell. I've been either working or playing so hard I haven't had much time to journal. Most of what I remember of the days since Christmas have to do with working in the crystallography lab.
A crystallography lab's main purpose in life is to discover the shape of protein molecules. We do it by bouncing X-rays off them. One protein molecule doesn't reflect enough X-rays to notice--we get around that by coaxing proteins to crystallize--this lines up ranks and ranks of proteins all facing the same way and a constant distance from each other (imagine a battalion of soldiers grouped for inspection--now pretend that they have grav belts and the formation extends upward as well). From certain angles this array of protein molecules will reflect X-rays (this kind of reflection-from-an-array is called "diffraction"), producing X-ray spots that will show up on film (or nowadays on an electronic substitute for film called an "area detector"--bulkier and *much* more expensive in the short run, but much more capable too). These spots look and behave a bit like the flecks of rainbow that a cut-glass crystal hanging in a sunny window will throw on the opposite wall. From the positions and brightnesses of the X-ray spots it is sometimes possible to determine the shape of the protein.
Anyway--none of this will happen without protein crystals, and we spend a lot of our time coaxing proteins to crystallize. I spent 14 1/2 hours yesterday preparing a particular protein and coaxing it to crystallize. It will be weeks before I know whether it worked.
Protein crystalls are very fragile. If they dry out too much, they go away. Under the X-ray beam, they frequently get damaged by the radiation and go away. One way to get around both these problems is to flash-freeze the crystals. Unfortunately, for this to work, the fluid that permeates the crystals has to undergo a "glass transition." In other words, it has to become solid, without actually crystallizing (ice crystals would destroy the internal regular structure of the crystal that makes it diffract, and produce X-ray spots of their own that would make it impossible to be sure what spots were protein). One of the important tricks for getting a glass transition is adding a cryoprotectant--a chemical like glycerol that interferes with water's ability crystallize.
I've been doing X-ray studies of a series of crystals in the past few days and I just realized yesterday I forgot to add cryoprotectant before I froze them. Damn and double damn. I don't know why I didn't see ice spots and finding out will require 'fessing up my stupid mistake to some more senior crystallographer. Bleagh.
In other news I have been playing with my new mp3-recorder a lot--I listen to the radio driving to work (because I'm not home in time--or even off work in time--to listen to the evening news anymore most days), and listen to mp3s driving home. I try to keep the volume low enough that I can still hear the traffic, but it's a 40 minute drive and I just can't resist my new toy.
On the bad side, one of the things I did in my busy and long day yesterday was walk smack into the corner of a lab bench as I was hurrying to wash something out. My recorder was in my pocket, and prevented a nasty bruise. Unfortunately it wasn't made to be smashed on a corner with the weight of my fast-moving thigh behind it--and I broke the faceplate :`(. I didn't cry--I was at work and I didn't have time. But I wanted to.
On the bright side, it still works--plays, records, plays the radio, navigates through its files and folders. I don't have anything to check the optical in/out--but I don't expect a problem. But it doesn't look as nice with its cracked, starred face plate, and I'm a little worried that sharp fragments might come off it and damage me or the LCD screen below it. I tried to call iRiver to find out if it could be repaired, but didn't have time at the lab to wait more than 20 minutes on hold, so I couldn't get through. I expect a lot of people got iRivers for Christmas and customer support is pretty busy. I doubt there's much point in calling today but Kip has promised to call for me tomorrow.
And I was so busy yesterday I didn't have time to practice the mandolin at all. :-( I didn't get home from work until nearly 11:30pm. By the time the New Year's bells were ringing I was in bed.
Here's hoping for scientific success, financial prosperity, good health and musical creativity in the new year!
A crystallography lab's main purpose in life is to discover the shape of protein molecules. We do it by bouncing X-rays off them. One protein molecule doesn't reflect enough X-rays to notice--we get around that by coaxing proteins to crystallize--this lines up ranks and ranks of proteins all facing the same way and a constant distance from each other (imagine a battalion of soldiers grouped for inspection--now pretend that they have grav belts and the formation extends upward as well). From certain angles this array of protein molecules will reflect X-rays (this kind of reflection-from-an-array is called "diffraction"), producing X-ray spots that will show up on film (or nowadays on an electronic substitute for film called an "area detector"--bulkier and *much* more expensive in the short run, but much more capable too). These spots look and behave a bit like the flecks of rainbow that a cut-glass crystal hanging in a sunny window will throw on the opposite wall. From the positions and brightnesses of the X-ray spots it is sometimes possible to determine the shape of the protein.
Anyway--none of this will happen without protein crystals, and we spend a lot of our time coaxing proteins to crystallize. I spent 14 1/2 hours yesterday preparing a particular protein and coaxing it to crystallize. It will be weeks before I know whether it worked.
Protein crystalls are very fragile. If they dry out too much, they go away. Under the X-ray beam, they frequently get damaged by the radiation and go away. One way to get around both these problems is to flash-freeze the crystals. Unfortunately, for this to work, the fluid that permeates the crystals has to undergo a "glass transition." In other words, it has to become solid, without actually crystallizing (ice crystals would destroy the internal regular structure of the crystal that makes it diffract, and produce X-ray spots of their own that would make it impossible to be sure what spots were protein). One of the important tricks for getting a glass transition is adding a cryoprotectant--a chemical like glycerol that interferes with water's ability crystallize.
I've been doing X-ray studies of a series of crystals in the past few days and I just realized yesterday I forgot to add cryoprotectant before I froze them. Damn and double damn. I don't know why I didn't see ice spots and finding out will require 'fessing up my stupid mistake to some more senior crystallographer. Bleagh.
In other news I have been playing with my new mp3-recorder a lot--I listen to the radio driving to work (because I'm not home in time--or even off work in time--to listen to the evening news anymore most days), and listen to mp3s driving home. I try to keep the volume low enough that I can still hear the traffic, but it's a 40 minute drive and I just can't resist my new toy.
On the bad side, one of the things I did in my busy and long day yesterday was walk smack into the corner of a lab bench as I was hurrying to wash something out. My recorder was in my pocket, and prevented a nasty bruise. Unfortunately it wasn't made to be smashed on a corner with the weight of my fast-moving thigh behind it--and I broke the faceplate :`(. I didn't cry--I was at work and I didn't have time. But I wanted to.
On the bright side, it still works--plays, records, plays the radio, navigates through its files and folders. I don't have anything to check the optical in/out--but I don't expect a problem. But it doesn't look as nice with its cracked, starred face plate, and I'm a little worried that sharp fragments might come off it and damage me or the LCD screen below it. I tried to call iRiver to find out if it could be repaired, but didn't have time at the lab to wait more than 20 minutes on hold, so I couldn't get through. I expect a lot of people got iRivers for Christmas and customer support is pretty busy. I doubt there's much point in calling today but Kip has promised to call for me tomorrow.
And I was so busy yesterday I didn't have time to practice the mandolin at all. :-( I didn't get home from work until nearly 11:30pm. By the time the New Year's bells were ringing I was in bed.
Here's hoping for scientific success, financial prosperity, good health and musical creativity in the new year!
![[identity profile]](https://www.dreamwidth.org/img/silk/identity/openid.png){kind=small}
iRiver
Date: 2004-01-01 08:47 am (UTC)I hope you can get the face plate fixed *hugs*
Re: iRiver
Date: 2004-01-02 09:05 pm (UTC)I need to send them e-mail and find out if I can hold off on mailing it in till after GaFilk, since the chance I'll get the replacement before GaFilk is minimal and one of the things I really want to do with it is record GaFilk :-)